CLEARWATER — After months of discord between his church and the city, Church of Scientology leader David Miscavige reached out this week to Clearwater leaders, arranging a sit-down in the church's Fort Harrison Hotel to iron out their differences.

The hour-long meeting between City Manager Bill Horne and Miscavige on Thursday included discussion of long-simmering issues between Clearwater and the church, which makes its spiritual home in Tampa Bay's third-largest city.

On the table: tension in the months leading up to the opening of the church's massive Flag Building downtown last fall, and raw feelings over possible locations for a downtown parking garage.

"His interest was — in light of everything that has happened — how do we move forward? That was the tone of the meeting," Horne said.

The church did not respond to a call and email seeking comment.

Mayor George Cretekos also had a brief meeting with Miscavige and said he was encouraged by the encounter.

Cretekos' five-minute "meet and greet" was his first glimpse of Miscavige in the flesh, despite having served nearly four decades as a top aide to the late U.S. Rep. C.W. Bill Young and another seven years on the Clearwater City Council.

"Now, at least, we've made face-to-face contact," Cretekos said. "Hopefully, we can follow up and discuss issues and concerns between the church and our community."

Miscavige agreed to keep in touch, Cretekos said.

Miscavige also thanked Cretekos for his December note congratulating the church on opening the Flag Building, considered by Scientologists to be their cathedral.

Cretekos complimented the church on its new park next to the Fort Harrison.

Horne hadn't talked with Miscavige in about three years before the Scientology leader called him to suggest a meeting.

"The last time we met was a little rocky," Horne said,referring to a 2011 meeting with Miscavige and former Mayor Frank Hibbard in which Miscavige became irritated during the discussion. "This time, it was a positive meeting."

Horne and Miscavige discussed where the city and the Clearwater Marine Aquarium want to build a downtown parking garage. The city and the aquarium had publicly identified a one-acre parcel on Drew Street, on the northern edge of downtown, as their first choice. But before they got around to buying, the Church of Scientology snapped it up, surprising aquarium and city leaders.

Earlier this year, the church refused to discuss parting with the property, prompting the city and aquarium to begin looking elsewhere, including a spot next door to the Flag Building.

Horne told the Tampa Bay Times recentlythat the city might pursue building a garage with 10 stories or more on a county-owned site across a side street from the seven-story, 300,000-square-foot Flag Building. The city's codes don't have any height restrictions downtown, Horne noted, which would allow the city and aquarium to build as "high as we want."

Miscavige told Horne on Thursday that he would reconsider the church's position against letting go of its Drew Street property.

"He said he would take a look at it," Horne said.

Miscavige also "expressed some concerns" over the way the church was portrayed in a three-month battle with the city last year. The city and church clashed over delays in opening the Flag Building, illegal tree cuttings and a massive tent downtown that violated the city's sign code.

But many of Miscavige's complaints were directed at the Times, Horne said.

"He was complaining about you guys more than anything," he said.

The Times covered the disputes in news stories.

After such a long freeze in relations, Horne said he was optimistic that the city could work with the church again.

"I think there's some opportunity, one of which is, maybe we can get the site we really want to build a garage," Horne said.

Charlie Frago can be reached at cfrago@tampabay.com or (727) 445-4159. Follow him on Twitter @CharlieFrago